research: finalize the thesis framing (aims + kappa)

[davorrunje]

Context

research-init adopt (#136) scaffolded the thesis-by-publication tree under docs/research/thesis/ with a framing draft (aims.md, kappa/kappa.md, milestones.yml). The aims, narrative through-line, and chapter↔paper map were drafted by the skill and are not yet author-owned/signed; the author asked to discuss the thesis framing as a follow-up rather than settle it during onboarding.

Goal

Settle the thesis framing with the author: finalize the aims, the narrative through-line, the chapter↔paper coverage map, and the institution milestones — then record it via the honest-scholar thesis skill.

Where

• docs/research/thesis/aims.md (aims + through-line + chapter↔paper map; currently readiness: framing).
• docs/research/thesis/kappa/kappa.md (synthesis scaffold; blockers: notes aim-3 uncovered).
• docs/research/thesis/milestones.yml (institution gates — currently template defaults).
• docs/research/papers.md (covers column must agree with the aims).

Proposed approach

Use the honest-scholar thesis skill (framing mode) to refine — don't churn — the aims; confirm the aim-1/2/3 decomposition (construction → characterization → applications) or revise; fill milestones.yml with the real institution deadlines; keep aims.md/papers.md covers consistent. Defensibility sign-off stays out of scope (aim-3 is uncovered).

Acceptance criteria

• Aims + through-line confirmed by the author (or revised).
• Chapter↔paper map in aims.md agrees with papers.md covers.
• milestones.yml reflects the real program deadlines.
• dashboard.md regenerated.

References

• chore: adopt honest-scholar as the research-workflow driver (install + research-init adopt) #136
• docs/research/thesis/, docs/research/papers.md